Combining NMR Spectroscopy and Molecular Dynamic Simulations to Solve and Analyze the Structure of Protein-RNA Complexes

Methods Enzymol. 2019:614:393-422. doi: 10.1016/bs.mie.2018.09.002. Epub 2018 Dec 10.


Understanding the RNA binding specificity of protein is of primary interest to decipher their function in the cell. Here, we review the methodology used to solve the structures of protein-RNA complexes using solution-state NMR spectroscopy: from sample preparation to structure calculation procedures. We also describe how molecular dynamics simulations can help providing additional information on the role of key amino acid side chains and of water molecules in protein-RNA recognition.

Keywords: MD simulation; Protein–RNA interactions; Solution-state NMR; Structures.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • CELF Proteins / chemistry*
  • CELF Proteins / metabolism
  • Humans
  • Hydrogen Bonding
  • Magnetic Resonance Spectroscopy / methods*
  • Molecular Dynamics Simulation*
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • RNA / chemistry*
  • RNA / genetics
  • RNA / metabolism
  • RNA Splicing Factors / chemistry*
  • RNA Splicing Factors / metabolism
  • Thermodynamics


  • CELF Proteins
  • RBFOX1 protein, human
  • RNA Splicing Factors
  • RNA